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Tripal v1.0 (6.x-1.0)
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Tripal v1.0 (6.x-1.0)
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Functions | |
| tripal_feature_analysis_get_property ($analysis_id=NULL, $feature_id=NUll, $analysisfeature_id=NULL, $property, $cv_name= 'tripal') | |
| tripal_feature_analysis_insert_property ($analysis_id=NULL, $feature_id=NUll, $analysisfeature_id=NULL, $property, $value, $update_if_present=0, $cv_name= 'tripal') | |
| tripal_feature_analysis_update_property ($analysis_id=NULL, $feature_id=NUll, $analysisfeature_id=NULL, $property, $value, $insert_if_missing=0, $cv_name= 'tripal') | |
| tripal_feature_analysis_update_property_by_id ($analysisfeatureprop_id, $property, $value, $cv_name= 'tripal') | |
| tripal_feature_analysis_delete_property ($analysis_id=NULL, $feature_id=NUll, $analysisfeature_id=NULL, $property, $cv_name= 'tripal') | |
| tripal_feature_analysis_delete_property_by_id ($analysisfeatureprop_id) | |
| tripal_feature_get_property ($feature_id, $property, $cv_name='tripal') | |
| tripal_feature_insert_property ($feature_id, $property, $value, $update_if_present=0, $cv_name= 'tripal') | |
| tripal_feature_update_property ($feature_id, $property, $value, $insert_if_missing=0, $cv_name= 'tripal') | |
| tripal_feature_update_property_by_id ($featureprop_id, $property, $value, $cv_name= 'tripal') | |
| tripal_feature_delete_property ($feature_id, $property, $cv_name='tripal') | |
| tripal_feature_delete_property_by_id ($featureprop_id) | |
| tripal_feature_reverse_complement ($sequence) | |
| tripal_feature_get_formatted_sequence ($feature_id, $feature_name, $num_bases_per_line, $derive_from_parent, $aggregate, $output_format, $upstream, $downstream, $sub_features=array()) | |
| tripal_feature_get_feature_relationships ($feature) | |
| tripal_feature_analysis_delete_property | ( | $ | analysis_id = NULL, |
| $ | feature_id = NUll, |
||
| $ | analysisfeature_id = NULL, |
||
| $ | property, | ||
| $ | cv_name = 'tripal' |
||
| ) |
Delete an analysis feature property using the property name. Use this when a property only exists once for a given analysis feature. When more than one value can exist for the same property use the tripal_feature_analysis_delete_property_by_id() function.
| $analysis_id | The analysis ID for the analysis feature. This argument is optional but if specified it must also be accompanied with a feature ID. |
| $feature_id | The feature ID for the analysis feature. This argument is optional but if specified it must also be accompanied with an analysis ID. |
| $analysisfeature_id | The analysis feature ID for the analysis feature. This argument is optional and can be used rather than specifying the $analysis_id and $feature_id arguments. If all three arguments are specified (e.g. an $analysis_id, $feature_id and $analysisfeature_id, then the $analysisfeature_id is used and the other two arguments are ignored. |
| $property | The cvterm name of the property to delete |
| $cv_name | Optional. The name of the cv to which the property belongs. By default this is the 'tripal' cv. |
Note: The property will be identified using the unique combination of the $analysis_id and $property and then it will be deleted
Definition at line 231 of file tripal_feature.api.inc.
{
// check that the incoming arguments are correct
if (($analysis_id and !$feature_id) or
(!$analysis_id and $feature_id)) {
watchdog('tripal_feature',
'tripal_feature_analysis_delete_property: Both an analysis ID and feature ID should be specified',
array(), WATCHDOG_WARNING);
}
// get the analysisfeature_id if one is not provided
if (!$analysisfeature_id) {
$columns = array('analysisfeature_id');
$values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
$result = tripal_core_chado_select('analysisfeature', $columns, $values);
$analysisfeature_id = $result[0]->analysisfeature_id;
}
// get the property.
return tripal_core_delete_property('analysisfeature', $analysisfeature_id, $property, $cv_name);
}
| tripal_feature_analysis_delete_property_by_id | ( | $ | analysisfeatureprop_id | ) |
Delete a property using the analysisfeatureprop_id
| $analysisfeatureprop_id | The analysis feature property ID for the analysis feature. |
Definition at line 263 of file tripal_feature.api.inc.
{
// get the property.
return tripal_core_delete_property_by_id('analysisfeature', $analysisfeatureprop_id);
}
| tripal_feature_analysis_get_property | ( | $ | analysis_id = NULL, |
| $ | feature_id = NUll, |
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| $ | analysisfeature_id = NULL, |
||
| $ | property, | ||
| $ | cv_name = 'tripal' |
||
| ) |
Retrieve properties from the analysisfeatureprop table for a feature.
| $analysis_id | The analysis ID for the analysis feature. This argument is optional but if specified it must also be accompanied with a feature ID. |
| $feature_id | The feature ID for the analysis feature. This argument is optional but if specified it must also be accompanied with an analysis ID. |
| $analysisfeature_id | The analysis feature ID for the analysis feature. This argument is optional and can be used rather than specifying the $analysis_id and $feature_id arguments. If all three arguments are specified (e.g. an $analysis_id, $feature_id and $analysisfeature_id, then the $analysisfeature_id is used and the other two arguments are ignored. |
| $property | The cvterm name of the properties to retrieve |
| $cv_name | Optional. The name of the cv to which the property belongs. By default this is the 'tripal' cv. |
Definition at line 36 of file tripal_feature.api.inc.
{
// check that the incoming arguments are correct
if (($analysis_id and !$feature_id) or
(!$analysis_id and $feature_id)) {
watchdog('tripal_feature',
'tripal_feature_analysis_get_property: Both an analysis ID and feature ID should be specified',
array(), WATCHDOG_WARNING);
}
// get the analysisfeature_id if one is not provided
if (!$analysisfeature_id) {
$columns = array('analysisfeature_id');
$values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
$result = tripal_core_chado_select('analysisfeature', $columns, $values);
$analysisfeature_id = $result[0]->analysisfeature_id;
}
// get the property.
return tripal_core_get_property('analysisfeature', $analysisfeature_id, $property, $cv_name);
}
| tripal_feature_analysis_insert_property | ( | $ | analysis_id = NULL, |
| $ | feature_id = NUll, |
||
| $ | analysisfeature_id = NULL, |
||
| $ | property, | ||
| $ | value, | ||
| $ | update_if_present = 0, |
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| $ | cv_name = 'tripal' |
||
| ) |
Insert a property for an analysis feature
| $analysis_id | The analysis ID for the analysis feature. This argument is optional but if specified it must also be accompanied with a feature ID. |
| $feature_id | The feature ID for the analysis feature. This argument is optional but if specified it must also be accompanied with an analysis ID. |
| $analysisfeature_id | The analysis feature ID for the analysis feature. This argument is optional and can be used rather than specifying the $analysis_id and $feature_id arguments. If all three arguments are specified (e.g. an $analysis_id, $feature_id and $analysisfeature_id, then the $analysisfeature_id is used and the other two arguments are ignored. |
| $property | The cvterm name of the property to insert |
| $value | The value of the property to insert |
| $update_if_present | A boolean indicated whether to update the record if it's already present |
| $cv_name | Optional. The name of the cv to which the property belongs. By default this is the 'tripal' cv. |
Definition at line 89 of file tripal_feature.api.inc.
{
// check that the incoming arguments are correct
if (($analysis_id and !$feature_id) or
(!$analysis_id and $feature_id)) {
watchdog('tripal_feature',
'tripal_feature_analysis_insert_property: Both an analysis ID and feature ID should be specified',
array(), WATCHDOG_WARNING);
}
// get the analysisfeature_id if one is not provided
if (!$analysisfeature_id) {
$columns = array('analysisfeature_id');
$values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
$result = tripal_core_chado_select('analysisfeature', $columns, $values);
$analysisfeature_id = $result[0]->analysisfeature_id;
}
// insert the property.
return tripal_core_insert_property('analysisfeature', $analysisfeature_id,
$property, $cv_name, $value, $update_if_present);
}
| tripal_feature_analysis_update_property | ( | $ | analysis_id = NULL, |
| $ | feature_id = NUll, |
||
| $ | analysisfeature_id = NULL, |
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| $ | property, | ||
| $ | value, | ||
| $ | insert_if_missing = 0, |
||
| $ | cv_name = 'tripal' |
||
| ) |
Update an analysis feature property using the property name. Use this when a property only exists once for a given analysis feature. When more than one value can exist for the same property use the tripal_feature_analysis_update_property_by_id() function.
| $analysis_id | The analysis ID for the analysis feature. This argument is optional but if specified it must also be accompanied with a feature ID. |
| $feature_id | The feature ID for the analysis feature. This argument is optional but if specified it must also be accompanied with an analysis ID. |
| $analysisfeature_id | The analysis feature ID for the analysis feature. This argument is optional and can be used rather than specifying the $analysis_id and $feature_id arguments. If all three arguments are specified (e.g. an $analysis_id, $feature_id and $analysisfeature_id, then the $analysisfeature_id is used and the other two arguments are ignored. |
| $property | The cvterm name of the property to update |
| $value | The value of the property to update |
| $insert_if_missing | A boolean indicated whether to insert the record if it's absent |
| $cv_name | Optional. The name of the cv to which the property belongs. By default this is the 'tripal' cv. |
Note: The property will be identified using the unique combination of the $analysis_id and $property and then it will be updated with the supplied value
Definition at line 150 of file tripal_feature.api.inc.
{
// check that the incoming arguments are correct
if (($analysis_id and !$feature_id) or
(!$analysis_id and $feature_id)) {
watchdog('tripal_feature',
'tripal_feature_analysis_update_property: Both an analysis ID and feature ID should be specified',
array(), WATCHDOG_WARNING);
}
// get the analysisfeature_id if one is not provided
if (!$analysisfeature_id) {
$columns = array('analysisfeature_id');
$values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
$result = tripal_core_chado_select('analysisfeature', $columns, $values);
$analysisfeature_id = $result[0]->analysisfeature_id;
}
// update the property.
return tripal_core_update_property('analysisfeature', $analysisfeature_id, $property, $cv_name, $value, $insert_if_missing);
}
| tripal_feature_analysis_update_property_by_id | ( | $ | analysisfeatureprop_id, |
| $ | property, | ||
| $ | value, | ||
| $ | cv_name = 'tripal' |
||
| ) |
Update a property for an analysis feature using the analysisfeatureprop_id.
| $analysisfeatureprop_id | The analysis feature property ID for the analysis feature. |
| $property | The cvterm name of the property |
| $value | The value of the property |
| $cv_name | Optional. The name of the cv to which the property belongs. By default this is the 'tripal' cv. * |
Definition at line 192 of file tripal_feature.api.inc.
{
// update the property.
return tripal_core_update_property_by_id('analysisfeature',
$analysisfeatureprop_id, $property, $cv_name, $value);
}
| tripal_feature_delete_property | ( | $ | feature_id, |
| $ | property, | ||
| $ | cv_name = 'tripal' |
||
| ) |
Delete a given feature property using the property name. Only use this if the property is unique and only exists once for the feature.
| $feature_id | The feature_id of the property to delete |
| $property | The cvterm name of the property to delete |
| $cv_name | Optional. The name of the cv to which the property belongs. By default this is the 'tripal' cv. |
Note: The property will be identified using the unique combination of the $feature_id and $property and then it will be deleted
Definition at line 384 of file tripal_feature.api.inc.
{
return tripal_core_delete_property('feature', $feature_id, $property, $cv_name);
}
| tripal_feature_delete_property_by_id | ( | $ | featureprop_id | ) |
Delete a given feature property using the featureprop_id
| $featureprop_id | The feature_id of the property to delete |
Definition at line 398 of file tripal_feature.api.inc.
{
return tripal_core_delete_property_by_id('feature', $featureprop_id);
}
| tripal_feature_get_feature_relationships | ( | $ | feature | ) |
Using the tripal_core_expand_chado_vars function to retrieve a set of relationships can be very slow, especialy if there are many relationships This function is intended to help speed up the retrieval of relationships by only retrieving the base information for the relationship and returning an array with
| $feature | The feature object |
Definition at line 810 of file tripal_feature.api.inc.
{
// expand the feature object to include the feature relationships.
$options = array(
'return_array' => 1,
'order_by' => array('rank' => 'ASC'),
);
$feature = tripal_core_expand_chado_vars($feature, 'table',
'feature_relationship', $options);
// get the subject relationships
$srelationships = $feature->feature_relationship->subject_id;
$orelationships = $feature->feature_relationship->object_id;
// get alignment as child. The $feature->featureloc element
// is already populated from the alignment preprocess function
$feature = tripal_core_expand_chado_vars($feature, 'table', 'featureloc');
$cfeaturelocs = $feature->featureloc->feature_id;
if (!$cfeaturelocs) {
$cfeaturelocs = array();
}
elseif (!is_array($cfeaturelocs)) {
$cfeaturelocs = array($cfeaturelocs);
}
// prepare the SQL statement to get the featureloc for the
// feature in the relationships.
$connection = tripal_db_persistent_chado();
$psql = "
PREPARE sel_featureloc_preprocess_relationships (int, int) AS
SELECT
FL.featureloc_id, F.name as srcfeature_name, FL.srcfeature_id,
FL.feature_id, FL.fmin, FL.fmax, FL.strand, FL.phase
FROM featureloc FL
INNER JOIN feature F ON F.feature_id = FL.srcfeature_id
WHERE FL.feature_id = $1 and FL.srcfeature_id = $2
";
tripal_core_chado_prepare('sel_featureloc_preprocess_relationships', $psql, array('int', 'int'));
// combine both object and subject relationshisp into a single array
$relationships = array();
$relationships['object'] = array();
$relationships['subject'] = array();
// iterate through the object relationships
if ($orelationships) {
foreach ($orelationships as $relationship) {
$rel = new stdClass();
// get locations where the child feature and this feature overlap with the
// same landmark feature.
$rel->child_featurelocs = array();
foreach ($cfeaturelocs as $featureloc) {
$res = chado_query("EXECUTE sel_featureloc_preprocess_relationships (%d, %d)",
$relationship->subject_id->feature_id,
$featureloc->srcfeature_id->feature_id);
while ($loc = db_fetch_object($res)) {
// add in the node id of the src feature if it exists and save this location
$loc->nid = $featureloc->srcfeature_id->nid;
$rel->child_featurelocs[] = $loc;
}
}
$rel->record = $relationship;
// get the relationship and child types
$rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name));
$child_type = $relationship->subject_id->type_id->name;
// get the node id of the subject
$sql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
$n = db_fetch_object(db_query($sql, $relationship->subject_id->feature_id));
if ($n) {
$rel->record->nid = $n->nid;
}
if (!array_key_exists($rel_type, $relationships['object'])) {
$relationships['object'][$rel_type] = array();
}
if (!array_key_exists($child_type, $relationships['object'][$rel_type])) {
$relationships['object'][$rel_type][$child_type] = array();
}
$relationships['object'][$rel_type][$child_type][] = $rel;
}
}
// now add in the subject relationships
if ($srelationships) {
foreach ($srelationships as $relationship) {
$rel = new stdClass();
// get locations where this feature overlaps with the parent
$rel->parent_featurelocs = array();
foreach ($cfeaturelocs as $featureloc) {
$res = chado_query("EXECUTE sel_featureloc_preprocess_relationships (%d, %d)",
$relationship->object_id->feature_id,
$featureloc->srcfeature_id->feature_id);
while ($loc = db_fetch_object($res)) {
// add in the node id of the src feature if it exists and save this location
$loc->nid = $featureloc->srcfeature_id->nid;
$rel->parent_featurelocs[] = $loc;
}
}
$rel->record = $relationship;
$rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name));
$parent_type = $relationship->object_id->type_id->name;
// get the node id of the subject
$sql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
$n = db_fetch_object(db_query($sql, $relationship->object_id->feature_id));
if ($n) {
$rel->record->nid = $n->nid;
}
if (!array_key_exists($rel_type, $relationships['subject'])) {
$relationships['subject'][$rel_type] = array();
}
if (!array_key_exists($child_type, $relationships['subject'][$rel_type])) {
$relationships['subject'][$rel_type][$parent_type] = array();
}
$relationships['subject'][$rel_type][$parent_type][] = $rel;
}
}
return $relationships;
}| tripal_feature_get_formatted_sequence | ( | $ | feature_id, |
| $ | feature_name, | ||
| $ | num_bases_per_line, | ||
| $ | derive_from_parent, | ||
| $ | aggregate, | ||
| $ | output_format, | ||
| $ | upstream, | ||
| $ | downstream, | ||
| $ | sub_features = array() |
||
| ) |
Retrieves the sequence for a feature.
| $feature_id | The feature_id of the feature for which the sequence will be retrieved |
| $feature_name | The feature name. This will appear on the FASTA definition line |
| $num_bases_per_line | Indicate the number of bases to use per line. A new line will be added after the specified number of bases on each line. |
| $derive_from_parent | Set to '1' if the sequence should be obtained from the parent to which this feature is aligned. |
| $aggregate | Set to '1' if the sequence should only contain sub features, excluding intra sub feature sequence. For example, set this option to obtain just the coding sequence of an mRNA. |
| $output_format | The type of format. Valid formats include 'fasta_html', 'fasta_txt' and 'raw'. The format 'fasta_txt' outputs line breaks as tags and the entire return value is in a tag with a fixed-width font definition. 'fasta_txt' outputs line breaks with windows format carriage returns (e.g. ) with no other formatting. The raw format is simply the sequence with now FASTA formatting and no line breaks. |
| $upstream | An integer specifing the number of upstream bases to include in the output |
| $downstream | An integer specifying the number of downstream bases to include in the output. |
Definition at line 469 of file tripal_feature.api.inc.
{
// to speed things up we need to make sure we have a persistent connection
$connection = tripal_db_persistent_chado();
if (!$upstream) {
$upstream = 0;
}
if (!$downstream) {
$downstream = 0;
}
// prepare statements we'll need to use later
if (!tripal_core_is_sql_prepared('sequence_by_parent')) {
// prepare the queries we're going to use later during the render phase
// This SQL statement uses conditionals in the select clause to handle
// cases cases where the alignment is in the reverse direction and when
// the upstream and downstream extensions go beyond the lenght of the
// parent sequence.
$psql ='PREPARE sequence_by_parent (int, int, int) AS
SELECT srcname, srcfeature_id, strand, srctypename, typename,
fmin, fmax, upstream, downstream, adjfmin, adjfmax,
substring(residues from (adjfmin + 1) for (upstream + (fmax - fmin) + downstream)) as residues
FROM (
SELECT
OF.name srcname, FL.srcfeature_id, FL.strand,
OCVT.name as srctypename, SCVT.name as typename,
FL.fmin, FL.fmax,
CASE
WHEN FL.strand >= 0 THEN
CASE
WHEN FL.fmin - $1 <= 0 THEN 0
ELSE FL.fmin - $1
END
WHEN FL.strand < 0 THEN
CASE
WHEN FL.fmin - $2 <= 0 THEN 0
ELSE FL.fmin - $2
END
END as adjfmin,
CASE
WHEN FL.strand >= 0 THEN
CASE
WHEN FL.fmax + $2 > OF.seqlen THEN OF.seqlen
ELSE FL.fmax + $2
END
WHEN FL.strand < 0 THEN
CASE
WHEN FL.fmax + $1 > OF.seqlen THEN OF.seqlen
ELSE FL.fmax + $1
END
END as adjfmax,
CASE
WHEN FL.strand >= 0 THEN
CASE
WHEN FL.fmin - $1 <= 0 THEN FL.fmin
ELSE $1
END
ELSE
CASE
WHEN FL.fmax + $1 > OF.seqlen THEN OF.seqlen - FL.fmax
ELSE $1
END
END as upstream,
CASE
WHEN FL.strand >= 0 THEN
CASE
WHEN FL.fmax + $2 > OF.seqlen THEN OF.seqlen - FL.fmax
ELSE $2
END
ELSE
CASE
WHEN FL.fmin - $2 <= 0 THEN FL.fmin
ELSE $2
END
END as downstream,
OF.residues
FROM featureloc FL
INNER JOIN feature SF on FL.feature_id = SF.feature_id
INNER JOIN cvterm SCVT on SF.type_id = SCVT.cvterm_id
INNER JOIN feature OF on FL.srcfeature_id = OF.feature_id
INNER JOIN cvterm OCVT on OF.type_id = OCVT.cvterm_id
WHERE SF.feature_id = $3) as tbl1
';
$status = tripal_core_chado_prepare('sequence_by_parent', $psql, array('int', 'int', 'int'));
if (!$status) {
watchdog('tripal_views_handler_field_sequence',
"init: not able to prepare SQL statement '%name'",
array('%name' => 'sequence_by_parent'), 'WATCHDOG ERROR');
}
// this query is meant to get all of the sub features of any given
// feature (arg #1) and order them as they appear on the reference
// feature (arg #2).
$psql ='PREPARE sub_features (int, int) AS
SELECT SF.feature_id, CVT.name as type_name, SF.type_id
FROM feature_relationship FR
INNER JOIN feature SF on SF.feature_id = FR.subject_id
INNER JOIN cvterm CVT on CVT.cvterm_id = SF.type_id
INNER JOIN featureloc FL on FL.feature_id = FR.subject_id
INNER JOIN feature PF on PF.feature_id = FL.srcfeature_id
WHERE FR.object_id = $1 and PF.feature_id = $2
ORDER BY FL.fmin ASC';
$status = tripal_core_chado_prepare('sub_features', $psql, array('int', 'int'));
if (!$status) {
watchdog('tripal_views_handler_field_sequence',
"init: not able to prepare SQL statement '%name'",
array('%name' => 'ssub_features'), 'WATCHDOG ERROR');
}
$psql ='PREPARE count_sub_features (int, int) AS
SELECT count(*) as num_children
FROM feature_relationship FR
INNER JOIN feature SF on SF.feature_id = FR.subject_id
INNER JOIN cvterm CVT on CVT.cvterm_id = SF.type_id
INNER JOIN featureloc FL on FL.feature_id = FR.subject_id
INNER JOIN feature PF on PF.feature_id = FL.srcfeature_id
WHERE FR.object_id = $1 and PF.feature_id = $2';
$status = tripal_core_chado_prepare('count_sub_features', $psql, array('int', 'int'));
if (!$status) {
watchdog('tripal_views_handler_field_sequence',
"init: not able to prepare SQL statement '%name'",
array('%name' => 'count_sub_features'), 'WATCHDOG ERROR');
}
}
// if we need to get the sequence from the parent then do so now.
if ($derive_from_parent) {
// execute the query to get the sequence from the parent
$sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
$parents = chado_query($sql, $upstream, $downstream, $feature_id);
while ($parent = db_fetch_object($parents)) {
$seq = ''; // initialize the sequence for each parent
// if we are to aggregate then we will ignore the feature returned
// by the query above and rebuild it using the sub features
if ($aggregate) {
// now get the sub features that are located on the parent.
$sql = "EXECUTE sub_features (%d, %d)";
$children = chado_query($sql, $feature_id, $parent->srcfeature_id);
$sql = "EXECUTE count_sub_features (%d, %d)";
$num_children = db_fetch_object(chado_query($sql, $feature_id, $parent->srcfeature_id));
// iterate through the sub features and concat their sequences. They
// should already be in order.
$types = array();
$i = 0;
while ($child = db_fetch_object($children)) {
// if the callee has specified that only certain sub features should be
// included then continue of this child is not one of those allowed
// subfeatures
if (count($sub_features) > 0 and !in_array($child->type_name, $sub_features)) {
continue;
}
// keep up with the types
if (!in_array($child->type_name, $types)) {
$types[] = $child->type_name;
}
$sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
// if the first sub feature we need to include the upstream bases
if ($i == 0 and $parent->strand >= 0) { // forward direction
// -------------------------- ref
// ....----> ---->
// up 1 2
$q = chado_query($sql, $upstream, 0, $child->feature_id);
}
elseif ($i == 0 and $parent->strand < 0) { // reverse direction
// -------------------------- ref
// ....<---- <----
// down 1 2
$q = chado_query($sql, 0, $downstream, $child->feature_id);
}
// if the last sub feature we need to include the downstream bases
elseif ($i == $num_children->num_children - 1 and $parent->strand >= 0) { // forward direction
// -------------------------- ref
// ----> ---->....
// 1 2 down
$q = chado_query($sql, 0, $downstream, $child->feature_id);
}
elseif ($i == $num_children->num_children - 1 and $parent->strand < 0) { // reverse direction
// -------------------------- ref
// <---- <----....
// 1 2 up
$q = chado_query($sql, $upstream, 0, $child->feature_id);
}
// for internal sub features we don't want upstream or downstream bases
else {
$sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
$q = chado_query($sql, 0, 0, $child->feature_id);
}
while ($subseq = db_fetch_object($q)) {
// concatenate the sequences of all the sub features
if ($subseq->srcfeature_id == $parent->srcfeature_id) {
$seq .= $subseq->residues;
}
}
$i++;
}
}
// if this isn't an aggregate then use the parent residues
else {
$seq = $parent->residues;
}
// get the reverse compliment if feature is on the reverse strand
$dir = 'forward';
if ($parent->strand < 0) {
$seq = tripal_feature_reverse_complement($seq);
$dir = 'reverse';
}
// now format for display
if ($output_format == 'fasta_html') {
$seq = wordwrap($seq, $num_bases_per_line, "<br>", TRUE);
}
elseif ($output_format == 'fasta_txt') {
$seq = wordwrap($seq, $num_bases_per_line, "\n", TRUE);
}
$residues .= ">$feature_name ($parent->typename) $parent->srcname:" . ($parent->adjfmin + 1) . ".." . $parent->adjfmax ." ($dir). ";
if (count($types) > 0) {
$residues .= "Excludes all bases but those of type(s): " . implode(', ', $types) . ". " ;
}
if ($parent->upstream > 0) {
$residues .= "Includes " . $parent->upstream . " bases upstream. ";
}
if ($parent->downstream > 0) {
$residues .= "Includes " . $parent->downstream . " bases downstream. ";
}
if (!$seq) {
if ($output_format == 'fasta_html') {
$residues .= "No sequence available.</br>";
}
else {
$residues .= "No sequence available.\n";
}
}
else {
if ($output_format == 'fasta_html') {
$residues .= "<br>";
}
$residues .= "\n" . $seq . "\n";
if ($output_format == 'fasta_html') {
$residues .= "<br>";
}
}
}
}
// if we are not getting the sequence from the parent sequence then
// use what comes through from the feature record
else {
$sql = "SELECT * FROM feature F WHERE feature_id = %d";
$values = db_fetch_object(chado_query($sql, $feature_id));
$residues = $values->residues;
if ($output_format == 'fasta_html') {
$residues = wordwrap($residues, $num_bases_per_line, "<br>", TRUE);
}
elseif ($output_format == 'fasta_txt') {
$residues = wordwrap($residues, $num_bases_per_line, "\n", TRUE);
}
$residues = ">$feature_name\n$residues\n";
}
// format the residues for display
if ($residues and $num_bases_per_line) {
if ($output_format == 'fasta_html') {
$residues = '<span style="font-family: monospace;">' . $residues . '</span>';
}
}
return $residues;
}
| tripal_feature_get_property | ( | $ | feature_id, |
| $ | property, | ||
| $ | cv_name = 'tripal' |
||
| ) |
Retrieve properties of a given type for a given feature
| $feature_id | The feature_id of the properties you would like to retrieve |
| $property | The cvterm name of the properties to retrieve |
| $cv_name | Optional. The name of the cv to which the property belongs. By default this is the 'tripal' cv. |
Definition at line 283 of file tripal_feature.api.inc.
{
return tripal_core_get_property('feature', $feature_id, $property, $cv_name);
}
| tripal_feature_insert_property | ( | $ | feature_id, |
| $ | property, | ||
| $ | value, | ||
| $ | update_if_present = 0, |
||
| $ | cv_name = 'tripal' |
||
| ) |
Insert a given property
| $feature_id | The feature_id of the property to insert |
| $property | The cvterm name of the property to insert |
| $value | The value of the property to insert |
| $update_if_present | A boolean indicated whether to update the record if it's already present |
| $cv_name | Optional. The name of the cv to which the property belongs. By default this is the 'tripal' cv. |
Definition at line 307 of file tripal_feature.api.inc.
{
return tripal_core_insert_property('feature', $feature_id, $property,
$cv_name, $value, $update_if_present);
}
| tripal_feature_reverse_complement | ( | $ | sequence | ) |
Performs a reverse compliment of a nucleotide sequence
| $sequence | The nucelotide sequence |
Definition at line 413 of file tripal_feature.api.inc.
{
$seq = strtoupper($sequence);
$seq = strrev($seq);
$seq = str_replace("A", "t", $seq);
$seq = str_replace("T", "a", $seq);
$seq = str_replace("G", "c", $seq);
$seq = str_replace("C", "g", $seq);
$seq = str_replace("Y", "r", $seq);
$seq = str_replace("R", "y", $seq);
$seq = str_replace("W", "w", $seq);
$seq = str_replace("S", "s", $seq);
$seq = str_replace("K", "m", $seq);
$seq = str_replace("M", "k", $seq);
$seq = str_replace("D", "h", $seq);
$seq = str_replace("V", "b", $seq);
$seq = str_replace("H", "d", $seq);
$seq = str_replace("B", "v", $seq);
return strtoupper($seq);
}
| tripal_feature_update_property | ( | $ | feature_id, |
| $ | property, | ||
| $ | value, | ||
| $ | insert_if_missing = 0, |
||
| $ | cv_name = 'tripal' |
||
| ) |
Update a feature property using the property name. Only use this if the property is unique and only exist once for the feature.
| $feature_id | The feature_id of the property to update |
| $property | The cvterm name of the property to update |
| $value | The value of the property to update |
| $insert_if_missing | A boolean indicated whether to insert the record if it's absent |
| $cv_name | Optional. The name of the cv to which the property belongs. By default this is the 'tripal' cv. |
Note: The property will be identified using the unique combination of the $feature_id and $property and then it will be updated with the supplied value
Definition at line 336 of file tripal_feature.api.inc.
{
return tripal_core_update_property('feature', $feature_id, $property, $cv_name, $value, $insert_if_missing);
}
| tripal_feature_update_property_by_id | ( | $ | featureprop_id, |
| $ | property, | ||
| $ | value, | ||
| $ | cv_name = 'tripal' |
||
| ) |
Update a given feature property using the featureprop_id
| $featureprop_id | The featureprop_id of the property to update |
| $property | The cvterm name of the property |
| $value | The value of the property |
| $cv_name | Optional. The name of the cv to which the property belongs. By default this is the 'tripal' cv. |
Definition at line 359 of file tripal_feature.api.inc.
{
return tripal_core_update_property_by_id('feature', $featureprop_id, $property, $cv_name, $value);
}
1.7.4